After hearing the recent podcast fleshing out the regions, a few ideas popped in my head to add to Naho and Motara.
Motara: I don’t have too much on Motara compared to Naho, so I’ll get it out of the way. The third Merchant King that Ahkmou overthrew was Pouks. Upon losing his domain, he looks for other means to retain his underworld ties. This leads him to the Brotherhood where he applies his former skills to aid this new group.
Naho: There was some discussion on whether Helryx or Tuyet fit better as the head arbiter, with the potential for one of them to drag Naho into the war. I’m not too familiar with either characters from G1, so I’ll stick with Helryx in this discussion. However, I have a possible alternative to who sparks Naho’s inclusion in the war.
It has been established that Gaaki had very strong ties to her region and no others. Joining the Brotherhood would have been a last resort in an attempt to find means to keep Naho secluded. Would it not make sense, then, that she continues to have some connection to her former region after becoming a Rahkshi? She will have her new ties to Makuta thanks to the Mask of Control, however, I believe her ties to Naho would still lie under the surface (water pun 
).
She could interact with Gali for the main story, but occasionally have secret meetings with the head arbiter, Helryx. These meetings would be her still trying to keep Naho pure and true to itself. So even with the mutation, Helryx would hear her out. During this time, I don’t think the Rahkshi threat would be well known to all the Matoran, so Helryx initially sees it as a fellow Nahoan who got into a tough spot for the sake of Naho.
“See Helryx? This is what interacting with the surface world does to you. I’m a monster now…”
Of course the Matoran realize the Rahkshi are evil after some time, thanks to seeing them attack the Toa/villages, but not before Guurak’s secret meetings persuaded Helryx to act. All for Naho. Bringing it back to the ancient glory of the former Atlantis-style city that they can’t access without water-breathing masks.
As a side note, I am still a strong supporter of Nahoans having natural water-breathing abilities without the need for a mask. With this in mind, I see another way to describe the whole “needs a mask to reach the city”.
In my pitch about mask powers (found here), the power I give to a lot of Nahoans is the Mask of Sonar. To tie this to having access to the underwater city, it could be that the city is so secluded from the surface that it’s difficult for even a Naho native to find it without some help. They would need a Mask of Sonar to locate the hidden city. Then when the masks get taken, the Naho Matoran can’t find it again, so they must make new cities (some even on the surface).
The natural water-breathing could also allow for some Nahoans to have never left the city when the masks were taken. They remained in the city since they would lose its location if they swam too far from it. These Nahoans would have been forgotten over time, and would be rediscovered when the masks come back. This could let some new characters come into the story, who have no ties to anything that has been going on above.